Did the show's writers not like that plot device so they changed it and hoped that no-one would remember it?
Since they planned out the overall story from start to finish before it even aired, I doubt that given his importance to the story.
In fact the ONLY glaring, disgusting, horrifying and all-around ugly blemish on the face of the series thus far, is the Desmond/medicine scene. I'm not talking prop mistakes, small details in real life (like the REAL flow of a court case), just pure, they fucked that up.
We see Desmond shooting up the Dharma meds in the season 2 opener. Then he later says they're no use because there's no sickness on the island.
What?
Just about everything else has a reasonable explanation. Even Charlie's, "I don't swim!"
edit:
By the way, I don't know if anyone here is a DarkUFO fan but they're an excellent Lost fansite that is pretty damn good about spoilers. Anyway, there's a poster there who does recaps, Vozzek69, who makes some really remarkable observations. I'm surprised he/she isn't a writer their self. Anyway, they have an interesting theory that grew from Daniel's card game which is that, everything on the island is constantly changing. Sometimes shit gets rearranged and they've pondered that maybe although it seems like simple bloopers, maybe sometimes it was meant to happen. The supporting evidence is intriguing as well culminating in Jin's famous, "Everything is going to change.", line. Anyway, I dunno whether that will actually go anywhere or not, but regardless his/her posts are really worth a read for serious fans. They're at DarkUFO with the title, "Things I Noticed".